The theme I am using is E17.
I also use a dark theme and have the same problem. This is fairly easy to solve though:
If the Server connection is open, close it (right click -> Disconnect server)
Right click on the Server connection and choose Properties...
In the Properties tab click the button in the the second to last item, named Colour
Select a new colour, say #3C3B37
You have to repeat the procedure for each and every Server connection, but it works.